Abstract
Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.
Highlights
Segregation distortion is the phenomenon in which alleles in the progeny of a cross between two varieties or species deviate from expected Mendelian ratios
We examined the performance of various p-value thresholds and multiple testing procedures on the detection of segregation distortion at a range of selection strengths, with a population of 1000 individuals per simulation (Fig 5). 56.1% of simulations contained significantly distorted markers when a p-value threshold of 0.05 was used with no selection, compared to 3% at p-value thresholds of p < 0.001, p < 0.05 (FDR corrected) and p < 0.05 (Bonferroni corrected)
It is clear a priori that when we test for segregation distortion, the probability of a false-positive result increases with the number of markers, as multiple inferences are being made simultaneously
Summary
Segregation distortion is the phenomenon in which alleles in the progeny of a cross between two varieties or species deviate from expected Mendelian ratios. The primary explanation of the cause of segregation distortion is a selection pressure operating against one of the parental alleles at some stage of the development cycle, whether at meiosis through meiotic drive [1], through male gamete competition [4], or at the level of the zygote. An example of this is the pollen killer gene in wheat [13], for which.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
